see what you should have done is pulled the engine to changie the timing belt ... then just scrapped it and got a real engine
... likea m20
I'm also using those plugs currently so I dont think thats the problem
maybe the coil took a dump?
did a vaccume line come loose after reassembly?
did the chain jump a tooth? if its just one tooth it may be better at some RPM and worse at others.. if you could check the timing that would clear that thought
sorry man thats all I can think of
and no worries its a M42 isnt it normal to be driving it past 4000 rpm :p